Time dependent fluorescence measurements

ABSTRACT

Methods and apparatus, including computer program products, implementing and using techniques for collecting optical data pertaining to one or more characteristics of a sample. The apparatus has a light source, one or more illumination optical elements, a scanner, one or more collection optical elements, and a device forming an aperture that limits detection of light from the sample. The illumination optical elements direct a light beam from the light source onto the sample. The scanner scans the light beam across the sample. The collection optical elements collect light from the sample and transmit the collected light to a detector. None of the collection optical elements are included among the illumination optical elements. The device forming an aperture limits detection of light from the sample to light associated with a limited vertical depth within the sample, and is one of the collection optical elements.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.10/927,748, filed on Aug. 26, 2004, and entitled “TIME DEPENDENTFLUORESCENCE MEASUREMENTS” which claims benefit of U.S. ProvisionalPatent Application No. 60/497,803, filed Aug. 26, 2003, entitled “LASERSCANNING METHOD FOR TIME DEPENDENT MEASUREMENT OF FLUORESCENCE,” and ofU.S. Provisional Patent Application No. 60/497,764, also filed Aug. 26,2003, and entitled “LASER SCANNING SYSTEM FOR TIME DEPENDENT MEASUREMENTOF FLUORESCENCE,” each of which are hereby incorporated by referenceherein.

BACKGROUND

This invention relates to measuring fluorescence and properties derivedfrom fluorescence in materials.

In conventional fluorescence microscopy, a sample, such as a biologicalspecimen is stained with fluorophores before being illuminated by lightof a relatively short wavelength. The illumination light, whichtypically is provided from a laser, excites the fluorophores into ahigher energy state where they remain for a short period of time, beforereturning to their original energy state while emitting fluorescentlight of a wavelength longer than the excitation wavelength. In afluorescence microscope, the emitted fluorescent light is collected byan objective lens of the microscope and is passed through the opticalsystem of the microscope, such that it can be viewed by a user, forexample, through the eyepieces of the microscope, or on a display screenof a video system that is connected to the microscope's optical system.In many cases, both the excitation light and the fluorescent light sharean optical path through the microscope's optical system, and can beseparated as needed, by optical components such as dichroic mirrors thatreflect light above the excitation wavelengths while passing theexcitation light.

The systems that have found most use in laboratories generally usevisible fluorescence of materials and visible light sources. The spatialresolution that can be obtained is determined by the specific opticalsetup. In some cases, the laboratory experimental setups use pulsedlaser light to improve the quality of the fluorescence image. Laboratoryarrangements are often used to detect biomolecular reactions andinteractions that can be probed by fluorescent methods. Fluorescent dyesare commonly used to examine cells by staining portions of the cells.For more routine imaging analyses, or assays, the excitation lightsource can illuminate a portion of an object to be examined, such as onemicrolocation in an array of microlocations.

For reasons of image contrast or signal discrimination, there is often aneed to improve the resolution and eliminate background noise in thefocal region of the sample that is being studied, as biological samplesin particular are fairly transparent and light collection over a toowide depth of focus may obscure the specific details that are beingstudied of the biological sample. Current solutions to this probleminclude confocal laser scanning microscopy or wide-field deconvolutiontechnologies, which generate optical “slices” or cross-sections thatinclude only the in-focus information. Another technique is the use oftwo-photon (2P) excitation produced by an infrared ultra-short, pulsedlaser beam. In two-photon systems, the pulsed laser allows the samefluorophores to be excited by photons of twice the wavelength than thoseused in single photon systems, but the longer wavelength photons are notabsorbed by the biological sample, which results in decreased toxicityto living cells and decreased photo bleaching. Furthermore, the infraredwavelength excitation significantly reduces scattering within thetissue, as the scattering coefficient is proportional to the inversefourth power of the excitation wavelength, resulting in penetrationdeeper into the specimen.

Fluorescent systems of this kind typically work well in laboratorysettings. However, in the chemical and biotechnology industry, there isoften a need to analyze a large number of samples in a time andcost-efficient manner, and due to the different requirements in theseenvironments, the above configurations are often not suitable orpossible to use. Therefore, what is needed is an improved apparatus thatcan be used to analyze an array of samples or objects in an efficientmanner, while having the ability to discriminate against backgroundnoise.

SUMMARY

In general, in one aspect, the invention provides methods and apparatus,including computer program products, implementing and using techniquesfor collecting optical data pertaining to one or more characteristics ofa sample. The apparatus has a light source, one or more illuminationoptical elements, a scanner, one or more collection optical elements,and a device forming an aperture that limits detection of light from thesample. The illumination optical elements direct a light beam from thelight source onto the sample. The scanner scans the light beam acrossthe sample. The one or more collection optical elements collect lightfrom the sample and transmit the collected light to a detector. None ofthe one or more collection optical elements are included among the oneor more illumination optical elements. The device forming an aperturelimits detection of light from the sample to light associated with alimited vertical depth within the sample, and is one of the collectionoptical elements.

Advantageous embodiments can include one or more of the followingfeatures. The device forming the aperture can be a slit aperture. Thedevice forming the aperture can be a bundle of optical fibers. Lightentering different optical fibers in the bundle of fibers can correspondto light at different vertical depths within the sample. The collectionoptical elements can collect light from a scan line on the sample withsubstantially uniform efficiency. The collection optical elements caninclude a cylindrical lens or a spherical lens.

Two or more detectors can be offset from one another with respect to apath for collecting the light from the sample, wherein each of the twoor more detectors can be positioned to capture light being emitted froma different vertical depth within the sample. There can be logic foradjusting the position of the sample with respect to the collectionoptical elements in response to light intensity detected at the two ormore detectors to maintain a substantially uniform vertical depth fromposition to position on the sample. The detector can include aphotomultiplier detector, a photodiode device, a charge coupled device,or a microchannel plate. Two or more detectors can be provided thatreceive light from the same region of the sample and detect two or moredifferent characteristics of the sample, such as different polarizationsof the light, different frequencies of the light and differentlifetimes. Logic can be provided for examining the correlation betweenthe signals obtained from the two or more detectors to identify objectsand exclude background noise.

The collection of optical data can be limited to regions of the sampleknown or detected to hold particular objects to be characterized on thesample, and the logic can be implemented in computer software orcomputer hardware instructions that can be read and executed by aprocessor operatively connected to the detector. The logic for limitingcollection of optical data can limit collection by only recordingoptical data when an intensity of the collected light is above a certainadjustable threshold value and the optical data meets at least oneadditional criterion. The logic for limiting collection of optical datacan limit collection by only recording optical data during time periodswhen the beam from the light source is scanned across an area ofinterest on the sample.

The light source can be a continuous wave laser, a pulsed laser, amode-locked high repetition rate laser, or a Q-switched laser. Thecontinuous wave laser can be a diode laser, a diode-pumped solid statelaser, a gas laser, or a tunable solid state laser system and can bemodulated in the frequency range of 1 kilohertz to 2 Gigahertz. Thepulsed laser can be configured to emit pulses in a frequency range of 1Hertz-100 Megahertz with a spacing ranging from 10 nanoseconds to 1second. The mode-locked laser can have a repetition rate that is higherthan or equal to 10 Megahertz. The Q-switched laser can be pulsed at afrequency in the range of 1 Hertz to 1 Megahertz. The light beam emittedfrom the light source can be intensity modulated in time with afrequency in the range of 1 Hertz to 2 Gigahertz.

The scanner can include one or more polygonal mirrors being rotated by ascanning element to scan the light beam across the sample. The scannercan include one or more mirrors being moved by a galvanometer to scanthe light beam across the sample. The scanner can be a resonant mirrorscanner. The one or more illumination optical elements can include atelecentric lens.

In general, in another aspect, the invention provides methods andapparatus, including computer program products, implementing and usingtechniques for collecting optical data pertaining to one or morecharacteristics of a sample. The apparatus has a light source, one ormore illumination optical elements, a scanner, and one or morecollection optical elements. The illumination optical elements direct alight beam from the light source of a first frequency onto the sample.The scanner scans the light beam across the sample. The collectionoptical elements collect light of a second frequency from the sample andtransmit the light to a detector. None of the one or more collectionoptical elements are included among the one or more illumination opticalelements.

In general, in another aspect, the invention provides methods andapparatus, including (computer program products, implementing and usingtechniques for collecting optical data pertaining to one or morecharacteristics of a sample. The apparatus has a light source, one ormore illumination optical elements for directing a light beam from thelight source onto the sample, a scanner for scanning the light beamacross the sample, one or more collection optical elements, a firstdevice that limits detection of light from the sample to lightassociated with a first vertical depth within the sample, and a seconddevice that limits detection of light from the sample to lightassociated with a second, different, vertical depth within the sample,where the first and second devices are collection optical elements.

Advantageous embodiments can include one or more of the followingfeatures. Logic can be included for automatically adjusting the verticalposition of the sample with respect to the collection optical elementsin response to the relative light intensity collected at the first andsecond devices in order to maintain a consistent vertical position ofthe sample with respect to the collection optical elements duringscanning. At least one of the first device and the second device can bean optical fiber. The first device can include a first row of opticalfibers and the second device can include a second row of optical fibers.The one or more detectors can include one or more microchannel platesarranged to separately detect light from the first and second devices.The one or more detectors can include a photomultiplier detector, aphotodiode device, a microchannel plate, or a charge coupled device. Twoor more detectors can be included for receiving light from the sampleand detecting two or more different characteristics of the light fromthe sample. The light beam from the light source can be monochromatichaving a first wavelength and wherein one or more of the collectionoptics and the one or more detectors is tuned to collect light at asecond wavelength, which is different from the first wavelength. A thirddevice can be included that limits detection of light from the sample tolight associated with a third, different, vertical depth within thesample.

The invention can be implemented to include one or more of the followingadvantages. Improved system and methods for cell and microarray analysisare provided. The use of a scanning light source, in combination withimproved geometry of the optical collection system, allows for manysamples or objects to be illuminated in a single scan. Furthermore, thesamples emit radiation in a specific confined region that is amenable todetection with characteristics that allow a higher degree of spatialresolution compared to several existing systems. The use of separateillumination optical components and separate collection opticalcomponents reduces the need to separate the illumination light from thefluorescent light emitted by the illuminated sample, and thus provides asimpler and more robust configuration. Using a cylindrical lens, such asa rod lens as one of the collection optical elements allows collectionof an entire scan line with substantially uniform efficiency.

The polarized nature of the light source can be used to examinereactivity, environment, and/or biological activity of either nativematerial or material that has been tagged with a fluorescent marker.

In one embodiment, the pulsed or modulated nature of the system allowsfor time dependent, rapid determination of chemically or photo-inducedbioactivity. The timing of the pulses, and the timing of the responsescan be used to extract physical information, such as fluorescencelifetimes and polarization relaxation times, as well as chemical orbiological information. With determinable characteristics of timeresolution coupled with the scanning feature, time-dependent informationcan be extracted, which can allow for precise mapping into a spatialdomain. The optical detection system confines the detection region insuch a way that an entire array can be scanned with a precisely locateddetection region without requiring a conventional autofocus mechanismfor the collection optics with the attendant timing requirements. Byusing an apparatus that allows for improved light collection efficiencyand background discrimination, the scanning source focus stays withinthe confined detection region. These characteristics of the inventionallow for mapping to a microlocation, either at the subcellular level orat a macro position within a microarray for rapid assay analyses.

The output signal is uniquely suited to analyzing the fluorescence ofcells and other objects or features within cells or in solution. Theoutput signal and its characteristic behavior can be analyzed todetermine structural, chemical, or biological properties of the object.An image of each object can be spectrally and/or temporally decomposedto discriminate object features by using polarization, fluorescencelifetime, or rotational correlation time as required. An object beingimaged in accordance with the present invention can be stimulated intofluorescence, either by autofluorescence, or by binding a molecule orprobe, that can be stimulated to fluoresce. Morphological and spectralcharacteristics of cells and sub-cellular features can be determined bymeasuring fluorescence signals that may also include time dependentspectral information, which can be used to determine time dependentcellular responses or other information about the cells and theircomponents. Similar measurements can be used to determine nuclearfluorescence intensity, cytoplasm fluorescence intensity, backgroundautofluorescence intensity, fluorescent depolarization intensity, andthe ratios of any of these values.

The output signal can also be used to monitor the sample's position, andif necessary readjust the position of the sample, such that an optimalamount of light is collected. The output signal can also be used toreduce the data storage requirements, for example, by only storing datawhen the intensity of the collected fluorescent light is above a certainthreshold value.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 is a schematic view of an apparatus for collecting optical datain accordance with a first embodiment of the present invention.

FIG. 2 is a side elevational view of a first embodiment of a scannerpart of the apparatus shown in FIG. 1.

FIG. 3 is a side elevational view of a second embodiment of a scannerpart of the apparatus shown in FIG. 1.

FIG. 4 is an isometric view of the scanner part shown in FIG. 2.

FIG. 5A is an isometric view of the scanner part shown in FIG. 3.

FIG. 5B is an isometric view of an apparatus for collecting optical datain accordance with the invention, with an alternative embodiment of thesample array.

FIG. 6 is a more detailed schematic view of the detection optics andelectronics system of an apparatus for collecting optical data inaccordance with the invention.

FIG. 7 is a schematic diagram showing a confined field of view for asingle detector configuration of the apparatus of FIG. 1.

FIG. 8 is a schematic diagram showing a more detailed view of theconfined field of view for a single detector configuration of FIG. 7.

FIG. 9 is a schematic diagram showing a confined field of view in astereo configuration of the apparatus of FIG. 1 with multiple detectors.

FIG. 10 is a schematic diagram showing multiple confined fields of viewfor an array of detectors of the apparatus of FIG. 1.

FIG. 11 is a schematic diagram showing output signals as a function oftime from three individual detectors in a multi-detector configurationof the apparatus of FIG. 1.

Like reference symbols in the various drawings indicate like elements.

DETAILED DESCRIPTION

The invention provides an improved apparatus that uses a scanning lightsource, which can be focused onto an array of samples or objects, withthe ability to discriminate against background noise or signal, andmakes use of image contrast mechanisms. The apparatus of the inventioncan be operated in several distinct modes or combinations thereof,depending on what type of sample data needs to be collected. Ahigh-level description of some exemplary modes will first be provided,followed by a more detailed discussion about the parts and geometry ofthe apparatus.

In a first mode, the output signal from the apparatus containsinformation such as the number of discrete positions in a cell or otherobject from which the fluorescent light originates, the relativelocation of the signal sources, and the color (e.g., wavelength orwaveband) of the light emitted at each position of the object. As aresult of the geometry of the illumination optics, a relatively largeillumination region is created that is confined to a region within thesample volume, thereby eliminating the need to have an apparatus whichmust adjust the focus of the illumination continuously and an in realtime over a plurality or an array of samples. The geometry of thecollection optics limits the detection region to a focal volume wherethe sample is contained and from which the data is collected. In oneembodiment, multiple collection arrangements are used with the attendantbenefits, which will be described below for a setup with two collectionlenses.

In a second mode, a plane-polarized laser beam can be propagated throughthe optical system onto the sample, allowing interrogation of thebiological material with polarized light. In this mode the emitted lightcan be separated into its two orthogonal components and analyzed eithersequentially in time with a switchable modulator, such as anelectrooptic modulator, to allow for detection of the parallel andperpendicular components, or simultaneously with multiple collectionoptics with specified perpendicular and parallel polarizing filters. Thepolarized nature of the excitation source allows for measurement ofproperties of biological materials where the characteristics of theanisotropy of the emission, or the time dependent nature of therelaxation of the polarization, can give rise to spatial or physicalinformation about the biological moiety.

In a third mode, several laser beams can be propagated through theoptical system onto the sample allowing interrogation of the biologicalmaterial with different wavelengths of light or with the same wavelengthat different times. In this mode the lasers can be pulsed simultaneouslyor with a fixed or variable delay between pulses. Delay between pulsesallows for measurement of properties of biological materials in anexcited state where the first laser pulse causes excitation of thebiological moiety and the second or additional laser pulses interrogatethat moiety in an excited state. The laser beams can be co-propagated sothat they focus on the same sample area during a scan or, alternatively,they can be propagated at some relative angle so that during a scan thelaser beams sequentially move over the same sample area.

In a fourth mode, a single modulated laser beam can be propagatedthrough the optical system onto the sample allowing lifetimemeasurements of the fluorescence in the biological material.

In a fifth mode, several detectors can be used in conjunction with onecollection optics arrangement, which creates multiple confinementregions for analysis, the advantages of which will be described infurther detail below.

In a sixth mode, several collection optics arrangements can be used toprovide improved confinement over a single collection optic with theunique geometry, or can be used to collect emission from the confinedregion with several characteristics which are uniquely specified to eachcollecting optics, the advantages which will be described below.

The apparatus will now be described in further detail, by way ofexample, with reference to FIGS. 1-11. As shown in FIG. 1, in oneembodiment, an excitation light source (1) emits excitation light (4) tobe projected onto a sample (2) that is to be investigated and whichrests on a microarray plate. Typically, the excitation light source (1)is a laser, such as an Ar or Ar/Kr mixed gas laser with excitation linesof 488, 514, 568 and 647 nm. In one embodiment, a continuous wave (CW)laser, such as the Compass 315 M laser from Spectraphysics Inc. ofMountain View, Calif., is used as an excitation source. Depending on thelaser (1) and specific optics used in the apparatus, the wavelength ofthe excitation light can be either within the visible range (i.e.,400-700 nm), or outside the visible range. For excitation wavelengthsbelow 400 nm photochemical reaction rates, such as those due tophotobleaching, tend to be substantial. In one embodiment, the outputfrom the laser (1) can be modulated and give information about the timedependent response of fluorescence signals by using a frequencymodulation detection scheme. In another embodiment, a pulsed laser withlaser pulses of approximately 12 ps FWHM (Full Width at Half Max) with aspacing of approximately 12 ns is used as the excitation light source(1). The average power of the laser (1) at the sample (2) is typicallyin the range 1 mW-1 W. The spacing of 12 ns is convenient forfluorescent lifetime detection, but can be varied as necessary, forexample, by varying the cavity length of the laser (1). Common to bothembodiments is the use of time-resolved imaging as a contrast producingagent. This has been developed significantly in the field offluorescence microscopy and has been described in detail by Marriott,Clegg, Arndt-Jovin, and Jovin, 1991, Biophys. J. 60:1374-1387; Verveer,Squire, and Bastiaens, 2000, Biophys. J. 78:2127-2137; Buehler, Dong,So, French, and Gratton, 2000, Biophys. J 79:536-549; Fushimi, Dix, andVerkman, 1991, Biophys. J. 57, 241-254; and Berndt, Gryczynski, andLakowicz, 1993, U.S. Pat. No. 5,196,709; as well as others notreferenced herein. The apparatus and methods used for such studies cangenerally be classified as one of two types: time-domain orfrequency-domain (see Hanley, Subramaniam, Arndt-Jovin, and Jovin, 2001,Cytometry 43:248-260). These apparatus and methods are well-known tothose skilled in the art.

After leaving the laser (1), the excitation light (4) passes through oneor more illumination optical elements to the sample (2). Theillumination optical elements include an electro-optic modulator (8), aset of beam-shaping lenses (3), a scanning device (5), and amulti-element lens (9). The electro-optic modulator (8) can be used topolarization modulate the excitation light (4), if required by theinvestigation that is to be carried out on the sample (2). The set ofbeam-shaping lenses (3) expands the laser beam in order to match theinput aperture of the scanning lens and provide the desired illuminationregion size at the sample (2). The scanning device (5) moves theexpanded laser beam back and forth in a line-scan over the sample (2)after the beam has been focused by the multi-element lens (9). Thescanning device (5), which will be described in further detail below,can be an electromechanical device coupled to an optic element, such asa mirror driven by a galvanometer. In one embodiment, which will also bedescribed in further detail below, the scanning device (5) uses apolygon with multiple reflective surfaces to scan the laser beam acrossthe sample (2). The multi-element lens (9) is designed to focus thelaser light at the operating wavelength of the laser (1). Themulti-element lens (9) can, for example, be a microscope objectivedesigned for the operating wavelength or a specially designed scanninglens, such as a telecentric lens, that has appropriate parameters toachieve a flat focal plane, for example, with a long working distanceand low first and second order aberrations, thus producing the same spotsize and shape over a wide range of positions (such as a scan line). Thetelecentric lens is particularly useful for covering a large field ofview.

After passing the multi-element lens (9), the beam (10) is focused ontoa region of the sample (2) to be imaged. The focal region is locatedabove, for example, a base of a microarray plate. The sample (2) can beobjects to be interrogated by fluorescence, such as cells attached tothe bottom of a microwell of the microarray plate.

The fluorescent light emitted by the sample (2) is collected by one ormore collection optical elements (19). As will be discussed below, thereare several ways to configure the collection optical elements (19) thatallow scanning of a large array, such as microarray plate. In oneembodiment, the collection optical elements (19) is a rod lens, designedto capture the entire range of sweep of the beam (10) over one dimensionof the base (11) of the sample array. The collection optical elements(19) can also include other types of lenses, or an aggregate of lenses,as would be determined by the specific information required from theemission. In some embodiments, multiple setups of collection opticalelements (19) can be used to improve collection efficiency.

The light collected by the collection optical elements (19) istransmitted to a detector (21) located at a convenient distance from thecollection optical elements (19). The transmission of the fluorescentlight can be accomplished by, for example, an optical fiber or a bundleof optical fibers (20). In one embodiment, the detector (21) is adetector with high gain, such as a photomultiplier tube, which producesan electrical output signal. The electrical output signal is furtherprocessed by a data acquisition system (14), which performs operationssuch as optimization of the gain and the signal to noise ratio (S/N), bymaking use of signal enhancing, averaging, or integrating detectionsystems.

FIG. 2 shows a side elevational view of the scanning portion of a firstembodiment of an apparatus in accordance with the invention. FIG. 4shows an isometric view of the scanning portion of the same embodimentof the apparatus. In the embodiment show in FIGS. 2 and 4, the scanningdevice (5) is a mirror (6) driven by a galvanometer. By moving themirror (6) back and forth using the galvanometer, the excitation light(10) from the laser (1) can be swept across the sample (2). FIGS. 3, 5Aand 5B show similar views of a second embodiment of an apparatus inaccordance with the invention, where the scanning device (5) instead isa polygon (7) with multiple reflective surfaces. In this embodiment thelaser beam (10) is swept over a region of the sample (2) by rotating thepolygon (7). In yet another embodiment, the scanning device (5) is aresonant scanning device, such as a mirror mounted on a torsion bar withelectromagnets causing the mirror to move back and forth. In allembodiments, the beam velocity across the sample (2) is thus a result ofthe rotation speed of the polygon (7) or the sweep velocity of thegalvanometer and the resonant scanning device, respectively. Each of thedifferent configurations has different advantages and drawbacks. Forexample, the galvanometer is less expensive than the polygon mirror, butoperates at a smaller angle and at a lower frequency, which causes aslower scanning speed. The resonant scanning device is cheaper than boththe galvanometer and the rotating mirror and operates at larger angles,but only operates at a predetermined frequency. The beam motion at thefocal plane in the sample (2) is typically 1-10 mm/ms, but can be asfast as 10-1000 mm/ms, depending on the sweep velocity of the mirror(6), or the rotation speed of the polygon (7). The polygon (7) istypically rotated at rotation speeds from 0.5 kHz to 20 kHz.

The multi-element lens (9) that receives the laser light (4) is designedto focus the laser light at the operating wavelength of the laser (1).The multi-element lens (9) focuses the laser light (4) close to thediffraction limit of the multi-element lens (9), which is typically inthe range of 5-20 microns, but can be as small or large as 1-200microns. The sample or sample array (2) is arranged to accept thefocused, beam at, or just above, the base (11) of the sample (2). Thelength of the scan line across the sample array (2) can be varied and istypically in the range 5 mm to 100 mm. In one embodiment, the scan light(10) can interrogate for example, a 96-well plate in less than oneminute at 5 micron resolution.

As can be seen in FIGS. 2-5, an optical element (12), such as a mirror,is provided approximately half way between the scan lens and the sampleto intercept and reflect a section of the incident light (10) onto adetector (13). Typically, the reflector (12) is located about 1-2 cmfrom the scan lens. The detector (13) is used to detect the location ofthe start of scan, in order to trigger the data acquisition system (14),which will be described in further detail below. The detector (13) can,for example, be a photodiode or equivalent component that can sense theincoming light (10) reflected from the reflector (12) and provide anelectrical signal to the data acquisition system (14). A second mirrorand detector can be placed on the other side of the scan line to detectthe end of a scan and thereby enable bidirectional scanning.

FIG. 7 shows an enlarged view of the sample (2), how incoming light (10)illuminates the sample (2), and a source region (17) from which thefluorescent light is collected in a single detector embodiment of theapparatus of FIG. 1. The sample (2) is located on a base (11) with aseries of optical elements (16) that allow the laser light (10) to betransmitted through to the sample contained in the array. The array can,for example, be a microarray plate containing wells with solutions orsamples adhered to the bottom of the wells. The focal plane location isnear the inner side of optical elements (16) and defines the region ofhighest light flux, thereby defining a region of highest emitted lightsource. The region's volume size depends on the multi-element lens (9)configuration and the depth of the interrogated sample (2) located abovethe base (11). The defined volume of a source region (17), whichactually gives rise to the fluorescent signal, additionally depends onthe configuration of the collection optical elements (19), as will nowbe discussed.

As can be seen in FIG. 7, the geometry of the collection opticalelements (19) is such that the collection region is confined to theregion of the field of view for the detector (21). The fluorescentsignal intensity is confined to a source region (17) formed by theintersection of the excitation source's focal region and the image ofthe detector (21) inside this region, as shown in FIG. 7. The sourceregion is located within a limited vertical depth of the sample, thatis, at a limited distance range above the base (11) upon which thesample (2) rests. A number of advantages result from arranging thecollection optical elements (19) such that a collection path (18) formsan angle with the incident light (10). Another advantage is theelimination of the need for optically flat micro arrays that do notdeviate in the location of surface apertures (16) of the well (2). Thecollection region is fixed or confined by the collection opticalelements (19) configuration so as to not be out of the focal plane ofthe system. Yet another advantage is that signal discrimination frombackground fluorescence in the sample well is much higher than thatobtained by a parallel collection system without eliminating orfiltering the fluorescent signal.

The emitted fluorescent light from the source region (17) is transmittedto the collection optical elements (19) along the collection path (18).The collection path (18) can extend through the optical element (16) inthe base (11) of the sample well, as shown in FIG. 7. In an alternativeembodiment, the collection path can extend through the well in thesample array to a location on the opposite side of the sample array, asshown in FIG. 1, for example. In both embodiments, the collectionoptical elements (19) are configured to collect and focus the lightemitted from the source region, as was described above.

There are several ways to configure the collection optical elements (19)that allow the scanning of a large array, such as a microarray plate.One geometry is shown in FIGS. 4, 5A and 5B. In this embodiment, thecollection optical elements (19) is a rod lens, which is designed tocapture the entire range of the sweep of the beam (10) over onedimension of the base of the sample array. The collection opticalelements (19) can include other types of lenses or lens combinations, aswould be determined by the specific information required from thefluorescent emission. As a result of light collimation by a singlecollection lens (19) as shown in FIGS. 4, 5A and 5B, all light emittedfrom a position on the array cell or microarray plate can be imaged, andcollected with high efficiency.

As can be seen in FIG. 8, another embodiment of the collection opticalelements (19) includes an optical transmission filter (23) and a slitaperture (26). Before passing the fluorescent light collected by the rodlens (19) to the detector (21), the light is appropriately filtered bythe transmission filter (23), which is designed to pass the fluorescenceemission. Alternatively, several filters can be chosen to minimize theamount of laser light to be detected by the detector (21). The opticalfilter (23) is chosen to optimize the collection of information withinthe spectral region of light emitted by the source region (17). Forexample, in one embodiment, the laser light is between 400 and 500 nm inwavelength, and the emitted fluorescence is in the region above 500 nm,and the optical filter (23) is a 500 nm long pass filter located behindthe rod lens (19). Many other configurations can be envisioned by peopleskilled in the art, depending on the wavelengths of the incident and theemitted light, and the filters chosen.

The slit aperture's (26) opening is located directly in front of theentrance to the detector (21) or optical fiber (20) coupled to thedetector (20). As can be seen in FIG. 8, the light that is emitted fromthe center of the source region (17) is collected by the rod lens (19)and passes through the center of the slit aperture (26). On the otherhand, light that is emitted from regions at a different depth of thesample, such as from the edge of the source region (17) will be imagedby the rod lens (19) outside the slit aperture's (26) opening, and willthus not be collected. The advantage of further confining the focalregion is that an improved spatial resolution will result, as well asfurther discrimination of background fluorescence outside of the region.In one embodiment, an aperture size of 250 microns results inapproximately a 400 micron detection region. As the skilled reader willrealize, combinations are also possible in which there is only anoptical transmission filter (23) or slit aperture (26), but not both.

In another embodiment, which is shown in FIG. 9, two or more collectionoptics arrangements (19 a, 19 b) are provided. With a stereoconfiguration of the collection lenses (19 a, 19 b) as shown in FIG. 9,the focal field for the two lenses can have improved confinement overthe single field generated by one lens and the focusing source shown anddiscussed above with respect to FIG. 8. The improvement is schematicallyrepresented in FIG. 9 by the intersection (22) of the focal planes forthe respective collection optics arrangements (19 a, 19 b),corresponding to the main object planes of the lenses (19 a, 19 b).

The setup of FIG. 9 with two sets of collection optics (19 a, 19 b) canalso be used for simultaneous collection of orthogonal components ofemission from a polarized excitation source. A first polarizing filter(23 a) can be used to pass only light of a first polarization to a firstdetector (21 a), and a second polarizing filter (23 b) can be used topass only light of a second, orthogonal, polarization to a seconddetector (21 b). The correlation of the signals collected in thisconfiguration, detection in the detection system, and subsequentmanipulation of the stored signal give rise to information not availableto a single detector, with attendant improvement in signal. Theinformation derived from this apparatus is steady-state anisotropy.Furthermore, with lifetime capability one can measure the correlation oftime dependent behavior of fluorescence anisotropy. Time-resolvedanisotropy of the emissions signal can give dynamical and/or structuralinformation on biomolecules and their environment. It is important thatany polarization filtering is performed before the collected lightenters any optical fibers, since the optical fibers distort thepolarization information and light that is output from an optical fiberdoes not have identical polarization components to the light that wasinput to the optical fiber at the other end.

As was discussed above, the detector (21) can be a detector with highgain, such as a photomultiplier tube (PMT). Other examples of detectorsare photodiodes, various types of charge coupled devices (CCDs), ormicrochannel plates. The detector (21) does not have to be physicallylocated adjacent to the collection optical elements (19), but the lightcan be transmitted from the collection optical elements (19) to thedetector (21) through a fiber array (20). In one embodiment, shown inFIG. 10, multiple detectors (21 a-21 c) are arranged adjacent to eachother in order to collect the signal from the collection opticalelements (19). In this case, the individual detectors (21 a-21 c) eachhave their own confined field of view, with the attendant advantagesassociated with the confined focal region as described above for onedetector. Just like with a single detector, the multiple detectors (21a-21 c) do not have to be physically located adjacent to the collectionoptical elements (19), but the light can be transmitted from thecollection optical elements (19) to each of the detectors (21 a-21 c)through a fiber array (20), or relay lens system for each detector. Thismulti-detector arrangement has additional advantages, such as theability to simultaneously detect signal at multiple locations, such asat different depths, within the source region (17) and to assign thesesignals to spatial locations within the sample (2). Alternatively, themultiple detectors (21 a-21 c) can be configured with optical filters(not shown in FIG. 10), and used to collect fluorescent emission fromdifferent spectral regions. In yet another embodiment, the multipledetectors (21 a-21 c) can be configured to detect orthogonalpolarization signals, as described above, allowing for simultaneousdetection of the anisotropy of the fluorescent signal.

The detectors (21 a-21 c) can also be used to correct the sampleposition based on the recorded signals, as can be seen in FIG. 11.Assume, for example, that it is desired to keep the sample (2) alignedwith the collection optics, so that most of the signal is received bythe middle detector (21 b). Since each detector (21 a-21 c) isassociated with a different depth, it can be expected that the middledetector (21 b) should have a signal that is higher than the outerdetectors (21 a, 21 c). As can be seen in FIG. 11, at time t0, only themiddle detector (21 b) registers a signal, whereas the outer detectors(21 a, 21 c) are not picking up any signals. At time t1, the sample's(2) physical position has shifted, such that only one of the outerdetectors (21 a) picks up a signal. This indicates that the sample (2)position must be adjusted, so the apparatus moves the sample (2) untilonly the middle detector (21 b) picks up a signal, as can be seen attime t2. At time t3, the sample (2) has moved again, but in this case inthe other direction, such that only the other outer detector (21 c)picks up a signal. This indicates that the sample (2) position must beadjusted in the other direction, and consequently the apparatus movesthe sample (2) until only the middle detector (21 b) again picks up thesignal, which can be seen at time t4. This technique can be used to movethe sample (2) not only in the vertical direction, but also in thehorizontal direction, depending on the detector arrangement. If multipledetector arrangements are used, such as in three orthogonal directions,complete control over the sample positioning can be achieved in allspatial directions. Since movement within a horizontal plane can occurwith two degrees of freedom, it is necessary to have two sets ofdetectors that preferably are oriented perpendicular to each otherwithin the horizontal plane. With this detector arrangement, ahorizontal translation of the sample will result in an increased signalin one or both detector sets, and the movement can be unambiguouslyidentified.

As can be seen in FIG. 1, the apparatus also contains logic, such as adata acquisition system (14), a data processing and storage system (24),and a controller (15), which work in conjunction with theabove-described optical and mechanical components of the apparatus toprovide adequate control capabilities for the various types ofinvestigations that can be carried out with the apparatus. The signalfrom the detector (21) is enhanced by the data acquisition system (14),and then stored into the data processing and storage system (24). Thedata processing and storage system (24) contains a fast A/D converter,or accepts digital information from the data acquisition system (14)directly. The data processing and storage system (24) can, for example,be a digitizing storage oscilloscope, or a computer with instructionsencoded in software for collecting and storing the detected or enhancedemission signal.

The signal can be labeled using a triggering event in time, and can beco-located with a spatial position of the fluorescing object within awell of a microarray, or with the macro location of the well in themicroarray plate. The software logic in the data processing and storagesystem (24) can contain instructions for deriving one or more objectcharacteristics from the emission signal, such as total intensity,average intensity, peak intensity, size, Gaussian or other waveform fit,or other such characteristics as may be found useful to those skilled inthe art. The trigger signal can be modified by the controller (15) asneeded to configure a delay, a blanking signal, a duty cycle, or providea means by which the trigger circuit of a boxcar averager, for example,can be activated. Two triggering events at the start and end of a scancan be used to measure the total scan time and correct for scan jitter.This also enables bidirectional scanning. There are many permutationsfor using this data processing and data storage system (24) that are notdescribed here, but which are useful to those skilled in the art.

In the interest of efficient data storage, due to the large size ofmulti-channel images, the data processing and storage system (24) can beset up such that data is only collected and saved when a relevant partof the sample (2), such as a cell, is illuminated. In one embodiment,this is accomplished by setting a threshold value in the data processingand storage system (24), and saving data only when the intensity of thecollected fluorescent light exceeds the threshold value for a certainperiod of time, or whenever some other pre-determined criterion issatisfied. In another embodiment, the data processing and storage system(24) only saves data during certain time intervals, such as when theilluminating beam (10) illuminates a well or a location in a microarray.Thus, instead of using intensity values to determine when to save data,the data is saved based on the positions of the light beam (10) at anygiven time, as determined by the scanner (5) and the multi-element lens(9).

In one embodiment, the apparatus allows for measurement of successivelaser pulses, as a result of modulating the laser light, over the samespatial location of the scan region and then subsequently analyzing thefluorescent signal measured by the detector (21) to determine atime-dependent response of the sample within the scanned region. Theresponse can include one or more characteristics of the sample, such asmolecular interactions, protein-protein interaction, binding kinetics,drug/target interactions, cell apoptosis, and so on. The timing andresponse to time dependent perturbations, such as the excitation pulse,form important aspects of this invention. The timing associated with theemission event with respect to the incident laser pulse, such as asignal timing or an emission lifetime, is captured by the configurationas described above. The detection of native or engineered materials willgive rise to information concerning chemical or biological activity, aswill be apparent to those skilled in the art, and the detection ofinduced or engineered fluorescence will also give rise to suchinformation as has been described above.

In another embodiment, the detector (21) can be arranged to collectinformation stored in the incident light as well as the emitted light,such as the polarization of the light. In this embodiment, the lightsource (1) is polarized, the incident polarization is determined, andthe fluorescent response emitted by the sample (2) is analyzed for itspolarization components, or anisotropy. The polarization of the incidentlight and/or the fluorescent light can be modulated, for example, by theelectrooptic device (8). The timing of the modulation of the polarizedsignals is controlled by the controller (15) with respect to the timingof the scans, so that quick, successive scans with orthogonalpolarization can be performed and so that dynamical information from thefluorescent polarization can be extracted. Furthermore, the intensity ofthe incident light can be modulated to collect time-dependentinformation from the sample. The detection of fluorescent polarizationand the time-dependence in materials gives rise to informationconcerning physical, chemical or biological activity, as will beapparent to those skilled in the art, and the detection of induced orengineered fluorescence polarization will also give rise to suchinformation as for example the result of a fluorescence polarizationimmunoassay, or other that has been described above.

In one embodiment, as shown in FIG. 6, the sample (2) can be placed on amoveable platform (25) that can be used to position the sample (2). Forexample, the platform can handle a microarray plate containing 96-samplewells, or a 3456-well plate for addressing very large arrays of testsand samples. A raster scan, or focused line of light (10) is provided tothe sample (2) and the emission is collected by the collection opticalelements (19) in such a way the arrays can be addressed in a parallelfashion. The parallel addressable nature of the invention allows forvery high throughput scanning and data collection, which is useful forexample, for interrogating and screening therapeutic effects ofchemicals on biomaterials as described above.

The platform (25) can be configured to move with a precision that iseither less than or on the order of the optical resolution of themulti-element lens (9), such that the motion of the platform (25) givesrise to high-resolution images of the sample (2). For example, thescanned beam (10) is swept across the sample (2) in one dimension andthe sample array is moved in a perpendicular direction to the sweep bythe platform (25), whereby the movement is timed such that the beammakes one or more complete excursions, and the emission signal from thedetector (21) derived from one or more complete sweeps is collected andsummed or manipulated by the data acquisition system (14) and the dataprocessing and storage system (24). In this embodiment, the platform(25) motion is perpendicular to the motion of the scan (10), such that atwo-dimensional image of the sample (2) can be reconstructed using theinstructions encoded in the data processing and storage system (24).

In another embodiment, the focus location of the multi-element lens (9)in the source region (17) can provide spatial information in thedirection perpendicular to the plane defined by the scan (10) andplatform (25) motion, resulting in a reconstructed 3-dimensional image.

In another embodiment, the time domain information reconstructed by thedata acquisition system (14) and the data processing and storage system(24) can be used to construct image spatial locations, which can giverise to information on the objects in sample array, such as events thatoccur as a result of the light probe. Alternatively, the information mayresult from, for example, non-light-induced drug or responses at thecellular or subcellular level.

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention. Forexample, the apparatus may perform the scanning function by moving thesample (2) only, instead of using a scanning device (5) to move the beam(4) from the light source (1) across the sample. The invention has beendescribed above with regards to fluorescent light, but the sameprinciples can be applied to the collection of phosphorescent light,which may be useful for investigations of certain samples. The inventioncan also be used to perform measurements of chemiluminescence andresonant energy transfers. Accordingly, other embodiments are within thescope of the following claims.

1. An apparatus for collecting optical data pertaining to one or morecharacteristics of a sample, the apparatus comprising: a light source;one or more illumination optical elements for directing a light beamfrom the light source onto the sample; a scanner for scanning the lightbeam across the sample; one or more collection optical elements forcollecting light from the sample and transmitting the collected light toa detector, wherein none of the one or more collection optical elementsare included among the one or more illumination optical elements; and adevice forming an aperture that limits detection of light from thesample to light associated with a limited vertical depth within thesample, wherein the device is one of the collection optical elements. 2.The apparatus of claim 1, wherein the device forming the aperture is aslit aperture.
 3. The apparatus of claim 1, wherein the device formingthe aperture is a bundle of optical fibers.
 4. The apparatus of claim 3,wherein light entering different optical fibers in the bundle of opticalfibers corresponds to light at different vertical depths within thesample.
 5. The apparatus of claim 1, wherein the collection opticalelements collect light from a scan line on the sample with substantiallyuniform efficiency.
 6. The apparatus of claim 5, wherein the collectionoptical elements include one of a cylindrical lens and a spherical lens.7. The apparatus of claim 1, further comprising two or more detectorsoffset from one another with respect to a path for collecting the lightfrom the sample, wherein each of the two or more detectors is positionedto capture light being emitted from a different vertical depth withinthe sample.
 8. The apparatus of claim 7, further comprising logic foradjusting the position of the sample with respect to the collectionoptical elements in response to light intensity detected at the two ormore detectors to maintain a substantially uniform vertical depth fromposition to position on the sample.
 9. The apparatus of claim 1, whereinthe detector includes at least one of: a photomultiplier detector, aphotodiode device, a charge coupled device, and a microchannel plate.10. The apparatus of claim 1, further comprising two or more detectorsfor receiving light from the same region of the sample and detecting twoor more different characteristics of the sample.
 11. The apparatus ofclaim 10, wherein the two or more different characteristics includedifferent polarizations of the light, different frequencies of thelight, and different lifetimes.
 12. The apparatus of claim 10, furthercomprising logic for examining the correlation between the signalsobtained from the two or more detectors to identify objects and excludebackground noise.
 13. The apparatus of claim 1, further comprising logicfor limiting collection of optical data to regions of the sample knownor detected to hold particular objects to be characterized on thesample, the logic being implemented in computer software or computerhardware instructions that can be read and executed by a processoroperatively connected to the detector.
 14. The apparatus of claim 13,wherein the logic for limiting collection of optical data limitscollection by only recording optical data when an intensity of thecollected light is above a certain adjustable threshold value.
 15. Theapparatus of claim 13, wherein the logic for limiting collection ofoptical data limits collection by only recording optical data duringtime periods when the beam from the light source is scanned across anarea of interest on the sample.
 16. The apparatus of claim 1, whereinthe light source is one of: a continuous wave laser, a pulsed laser, amode-locked high repetition rate laser, and a Q-switched laser.
 17. Theapparatus of claim 16, wherein the continuous wave laser is one of: adiode laser, a diode-pumped solid state laser, a gas laser, and atunable solid state laser system.
 18. The apparatus of claim 16, whereinthe continuous wave laser is modulated in a frequency range of 1kilohertz to 2 Gigahertz.
 19. The apparatus of claim 16, wherein thepulsed laser is configured to emit pulses in a frequency range of 1Hertz-100 Megahertz with a spacing ranging from 10 nanoseconds to 1second.
 20. The apparatus of claim 16, wherein the mode-locked laser hasa repetition rate that is higher than or equal to 10 Megahertz.
 21. Theapparatus of claim 16, wherein the Q-switched laser is pulsed at afrequency in the range of 1 Hertz to 1 Megahertz.
 22. The apparatus ofclaim 1, wherein the light beam emitted from the light source isintensity modulated in time with a frequency in the range of 1 Hertz to2 Gigahertz.
 23. The apparatus of claim 1, wherein the scanner includesone or more polygonal mirrors being rotated by a scanning element toscan the light beam across the sample.
 24. The apparatus of claim 1,wherein the scanner includes one or more mirrors being moved by agalvanometer to scan the light beam across the sample.
 25. The apparatusof claim 1, wherein the scanner is a resonant mirror scanner.
 26. Theapparatus of claim 1, wherein the one or more illumination opticalelements include a telecentric lens.
 27. An apparatus for collectingoptical data pertaining to one or more characteristics of a sample, theapparatus comprising: a light source; one or more illumination opticalelements for directing a light beam from the light source of a firstfrequency onto the sample; a scanner for scanning the light beam acrossthe sample; and one or more collection optical elements for collectinglight of a second frequency from the sample and transmitting the lightto a detector, wherein none of the one or more collection opticalelements are included among the one or more illumination opticalelements, and wherein the first and second frequencies are different.28. The apparatus of claim 27, wherein the collection optical elementsinclude one or more of a bandpass filter and a cutoff filter fordetermining the second frequency.
 29. The apparatus of claim 27, furthercomprising two or more detectors offset from one another with respect toa path for collecting the light from the sample, wherein each of the twoor more detectors is positioned to capture light being emitted from adifferent vertical depth within the sample.
 30. The apparatus of claim29, further comprising logic for adjusting the position of the samplewith respect to the collection optical elements in response to lightintensity detected at the two or more detectors to maintain asubstantially uniform vertical depth from position to position on thesample.
 31. The apparatus of claim 27, further comprising two or moredetectors for receiving light from the same region of sample anddetecting two or more different characteristics of the sample.
 32. Theapparatus of claim 31, wherein the two or more different characteristicsinclude different polarizations of the light, different frequencies ofthe light, and different lifetimes.
 33. The apparatus of claim 27,further comprising logic for limiting collection of optical data toregions of the sample known or detected to hold particular objects to becharacterized on the sample, the logic being implemented in computersoftware or computer hardware instructions that can be read and executedby a processor operatively connected to the detector.
 34. The apparatusof claim 27, wherein the logic for limiting collection of optical datalimits collection by only recording optical data when an intensity ofthe collected light is above a certain adjustable threshold value andthe optical data meets at least one additional criterion.
 35. Theapparatus of claim 27, wherein the logic for limiting collection ofoptical data limits collection by only recording optical data duringtime periods when the beam from the light source is scanned across anarea of interest on the sample.
 36. The apparatus of claim 27, whereinthe one or more collection optical elements include a device forming anaperture that limits detection of light from the sample to lightassociated with a limited depth of focus within the sample.
 37. Theapparatus of claim 27, wherein the device forming the aperture is a slitaperture.
 38. The apparatus of claim 27, wherein the device forming theaperture is a bundle of optical fibers.
 39. The apparatus of claim 38,wherein light entering different optical fibers in the bundle of fiberscorresponds to light at different vertical depths within the sample. 40.The apparatus of claim 27, wherein the one or more illumination opticalelements include a telecentric lens.
 41. An apparatus for collectingoptical data pertaining to one or more characteristics of a sample, theapparatus comprising: a light source; one or more illumination opticalelements for directing a light beam from the light source onto thesample; a scanner for scanning the light beam across the sample; one ormore collection optical elements for collecting light from the sampleand transmitting the collected light to one or more detectors; and afirst device that limits detection of light from the sample to lightassociated with a first vertical depth within the sample, a seconddevice that limits detection of light from the sample to lightassociated with a second, different, vertical depth within the sample,wherein the first and second devices are collection optical elements.42. The apparatus of claim 41, further comprising logic forautomatically adjusting the vertical position of the sample with respectto the collection optical elements in response to the relative lightintensity collected at the first and second devices in order to maintaina consistent vertical position of the sample with respect to thecollection optical elements during scanning.
 43. The apparatus of claim41, wherein at least one of the first device and the second device is anoptical fiber.
 44. The apparatus of claim 43, wherein the first devicecomprises a first row of optical fibers and the second device comprisesa second row of optical fibers.
 45. The apparatus of claim 41, whereinthe one or more detectors comprise one or more microchannel platesarranged to separately detect light from the first and second devices.46. The apparatus of claim 41, wherein the one or more detectorsincludes at least one of: a photomultiplier detector, a photodiodedevice, a microchannel plate, and a charge coupled device.
 47. Theapparatus of claim 41, further comprising two or more detectors forreceiving light from the sample and detecting two or more differentcharacteristics of the light from the sample.
 48. The apparatus of claim41, wherein the light beam from the light source is monochromatic havinga first wavelength and wherein one or more of the collection optics andthe one or more detectors is tuned to collect light at a secondwavelength, which is different from the first wavelength.
 49. Theapparatus of claim 41, further comprising a third device that limitsdetection of light from the sample to light associated with a third,different, vertical depth within the sample.